We have spots where some stones have fallen out - when the pool was newer we had a few of the little bits of stones that were picked up by the robot. I think this is due to the nature of all of those random shaped stones - some of them are going to be tapered just right so that they will easily fall out. The rest are captured well enough and hold in place well.
Our LED Lights do seem to magnify any imperfections and makes it easier to notice them, but I haven't picked up on missing stones from the lights. We have a really dark finish so it might show (or not show) missing stones differently than yours does.
Our floors are pretty smooth - in general they are just as smooth as the walls, so I expect that they just didn't do as good of a job polishing yours. That being said, I have noticed that the floor right near our 2 main drains is just a tiny bit rougher - this could be due the original acid wash - since that is where all of the liquid settled when they did the acid wash - it might have etched that area a bit more.
We had several areas on different walls that were rough and a little 120 grit sand paper fixed those right up. We also had another area on a step that the pebble company sanded down - I could see that spot for about 2 years, but looking for it the other day it has blended in as the surface has aged.
We have only used a nylon brush on ours - and most of our "brushing" is now done by our robot! I think the nylon would be good enough with the polished finish.
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Your pool looks great by the way.
We registered with WetEdge directly for the finish warranty. I hope we never need to use the warranty.